ones that spring to mind:
cave
dodonpachi end of stage bonus (not calculated properly in 2nd loop unless you play on the 2P side ???)
dodonpachi stage 5 boss freezes and doesn't shoot if you take his health bar below 50% while he's half off-screen
esprade boss milking (which i gather they knew existed, but didn't think anyone would suck enough to actually do it

guwange counter-stop
ketsui and the bouncing bomb

mushihimesama score boards do not save properly
mushihimesama crashes if you play the TLB with two players ???
espgaluda 2 demo bug, and green gems glitch on stage 2
pink sweets crashes on stage 6 / score attack mode
daifukkatsu counterstop on 1-5

only other ones that i can think of are bakraid's first version being counter-stopped (???), and mars matrix arcade being counter-stopped on stage 3

what other ones are there...?